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Crystal structure of burkholderia glumae toxa with bound S- adenosylhomocysteine (sah) and 1,6-didemethyltoxoflavin
Analyse Crystal structure of burkholderia glumae toxa with bound S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JE0
- Type
- protein
- Length
- 482 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl transferase
- UniProt
- Q9LBJ0
- Ligands
- SAH, AZ8
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methyl transferase | protein | 241 | 39% helix, 28% strand | Q9LBJ0 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- AZ8 · pyrimido[5,4-e][1,2,4]triazine-5,7(6H,8H)-dione · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.75 | 0.88 | 46 | SAH, AZ8 |
| 2 | 263 | 0.74 | 0.87 | 45 | SAH, AZ8 |
| 3 | 424 | 0.68 | 0.80 | 33 | empty |
| 4 | 158 | 0.59 | 0.83 | 20 | empty |
| 5 | 157 | 0.57 | 0.82 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 712 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5JE0 · Crystal structure of Burkholderia glumae ToxA with bound S-adenosylhomocysteine (SAH) and… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9LBJ0
- Elsewhere: RCSB PDB 5JE0 · PDBe 5JE0 · UniProt Q9LBJ0
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